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This is on Linux Mint 16 Cinnamon Edition 64, which I believe is quite close to Ubuntu.
I realise this section is for MAC but I wondered if this issue might be common to both platforms. I have suffered it with BC3 as well and have always had to work around it on Linux (but never on XP).

The number of simultaneous connections is 1 (unchanged from default).

If I monitor the number of open files on the process while comparing the local and remote directory trees it sits around 80-82. I haven't yet seen how or when it increases but at some point it stops comparing and trying to compare any individual file after this point results in "Too many open files". At this point the number of open files is 1093. I can test it again to see if this number is consistent.

The maximum number of open files on my system is 29,000 or thereabouts. I increased it to 60,000 to no effect - the comparison still seems to stop at the same point in the tree. As far as I can see there are no user-specific or process-specific limits imposed on the max open files.